115964ed-2427-4c4c-980a-e8fab4a4a92d - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001011335 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:We search for developmental changes specific to humans by examining gene expression profiles in the human, chimpanzee and rhesus macaque prefrontal and cerebellar cortex. In both brain regions, developmental patterns were more evolved in humans than in chimpanzees. The major human specific genes in prefrontal cortex was enriched in neuronal functions and regulated by several transcription factors, which were previously implicated in regulation of neuronal functions. To confirm neuronal function of the human prefrontal cortex specific genes, we identifed response genes upon neuronal activation in mouse cortical neurons. Our results show that human specific genes are enriched in the response genes upon neuronal activation, implying the function of human prefrontal cortex specific genes in synaptic development. The cortical neurons from E15 mouse were isolated and cultured. We then exposed neurons to bicuculline (Bic), or potassium chloride (KCl), or without treatment. The cultured neurons under each group were hybridized to Agilent whole mouse genome oligo microarray (4x44k).
2012-02-02 | E-GEOD-29139 | biostudies-arrayexpress
Project description:Fresh frozen post mortem prefrontal cortex tissue (Brodman area 46) was obtained from 44 individuals varying in age from 0 to 49 years. RNA was extracted from these samples and hybridized to HG133plus2.0 GeneChips. The data was used to examine patterns of gene expression over the course of human postnatal developmental and ageing. PMI - postmortem interval, DLPFC - dorsolateral prefrontal cortex Experiment Overall Design: The dataset consists of 44 individuals varying in age from 0 to 49 years
2009-12-02 | E-GEOD-13564 | biostudies-arrayexpress
Project description:Fresh frozen post mortem prefrontal cortex tissue (Brodman area 46) was obtained from 44 individuals varying in age from 0 to 49 years. RNA was extracted from these samples and hybridized to HG133plus2.0 GeneChips. The data was used to examine patterns of gene expression over the course of human postnatal developmental and ageing. PMI - postmortem interval, DLPFC - dorsolateral prefrontal cortex
2009-11-11 | GSE13564 | GEO
Project description:Protein from astrocytes (glial fibrillary acidic protein-positive cells), neurons (beta-III tubulin-positive cells), and unsorted (cell suspension without any enrichment based on astrocyte or neuron markers) from human, post-mortem Alzheimer's disease (AD) and aged-matched non-symptomatic (NS) prefrontal cortex brain samples.
2019-05-06 | MSV000083747 | MassIVE
Project description:Alcohol use disorder (AUD) affects transcriptomic, epigenetic and proteomic expression in several organs including the brain. Multi-omic analyses of the brain from individuals with AUD to date lack a comprehensive analysis of protein alterations in the multiple brain regions that underlie neuroadaptations occurring in AUD. We performed quantitative proteomic analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of human post-mortem tissue from brain regions that play a key role in the development and maintenance of AUD: amygdala (AMG), hippocampus (HIPP), hypothalamus (HYP), nucleus accumbens (NAc), prefrontal cortex (PFC) and ventral tegmental area (VTA). Brain tissues analyzed were from individuals with AUD (n = 11) and matched controls (n = 16).
2023-10-24 | PXD040884 | Pride
Project description:Profiling of paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen samples by bulk-tissue RNA-sequencing. Samples were derived from 4 post-mortem neuropathologically-confirmed control individuals ( anterior prefrontal cortex – 4 individuals, cerebellar cortex – 4 individuals, putamen- 3 individuals). Paired-end FASTQ files for each of the human samples are provided. Fastp (v 0.20.0), a fast all-in-one FASTQ pre-processor, was used for adapter trimming, read filtering and base correction. Fastp default settings were used for quality filtering and base correction. Further details on parameters used are available here: https://github.com/RHReynolds/RNAseqProcessing .
| EGAD00001009264 | EGA
Project description:Recent advances in chromatin architecture profiling technologies, such as single-cell Hi-C (scHi-C), allow us to dissect the heterogeneity of chromosome higher-order structures across diverse cell states and different individuals. However, scHi-C experiments are still expensive and not immediately available for population-scale profiling. Here, we present scENCORE, a computational method, to reconstruct personalized and cell-type-specific higher-order chromatin structures, such as A/B compartments, directly from more cost-effective and widely available single-cell epigenetic data (e.g., scATAC-seq). We apply scENCORE on scATAC-seq data from post-mortem prefrontal cortex brains and demonstrate its utility to 1) project Mega-base scale chromatin regions into lower dimensional space by leveraging graph embedding technologies based on cell-type-specific co-variability patterns, 2) define A/B compartments via unsupervised clustering, 3) perform an alignment algorithm for multi-graph embedding to derive comparable chromatin representations and highlight dynamic chromatin compartments across cell states and individuals. Validated by Hi-C experiments using FACS-sorted cells, scENCORE can faithfully reconstruct cell-type-specific chromatin compartments. Furthermore, scENCORE uniformly constructs chromosome conformation across population-scale scATAC-seq data and discovers key 3D structural switching events associated with psychiatric disorders. In summary, scENCORE allows cost-effective cell-type-specific and personalized reconstruction that delineate higher-order chromatin structures.
2023-09-27 | GSE216270 | GEO
Project description:Alzheimer’s disease (AD) is a chronic neurodegenerative disorder that is characterized by progressive neuropathology and cognitive decline. We performed a cross-tissue analysis of methylomic variation in AD using samples from three independent human post-mortem brain cohorts. We identified a differentially methylated region in the ankyrin 1 (ANK1) gene that was associated with neuropathology in the entorhinal cortex, a primary site of AD manifestation. This region was confirmed as being substantially hypermethylated in two other cortical regions (superior temporal gyrus and prefrontal cortex), but not in the cerebellum, a region largely protected from neurodegeneration in AD, or whole blood obtained pre-mortem from the same individuals. Neuropathology-associated ANK1 hypermethylation was subsequently confirmed in cortical samples from three independent brain cohorts. This study represents, to the best of our knowledge, the first epigenome-wide association study of AD employing a sequential replication design across multiple tissues and highlights the power of this approach for identifying methylomic variation associated with complex disease. For the first (discovery) stage of our analysis, we used multiple tissues from donors (N = 122) archived in the MRC London Brainbank for Neurodegenerative Disease. From each donor, we isolated genomic DNA from four brain regions (EC, superior temporal gyrus (STG), prefrontal cortex (PFC) and CER) and, where available, from whole blood obtained pre-mortem. Our analyses focused on identifying differentially methylated positions (DMPs) associated with Braak staging, a standardized measure of neurofibrillary tangle burden determined at autopsy.
2014-08-17 | E-GEOD-59685 | biostudies-arrayexpress
Project description:This study aims to profile transposable element expression in the different cell types of the prefrontal-cortex in human post-mortem samples
2023-02-10 | GSE211870 | GEO
Project description:This SuperSeries is composed of the following subset Series:; GSE5388: Adult postmortem brain tissue (dorsolateral prefrontal cortex) in subjects with bipolar disorder; GSE5389: Adult postmortem brain tissue (ortibtofrontal cortex) in subjects with bipolar disorder; Bipolar affective disorder is a severe psychiatric disorder with a strong genetic component but unknown pathophysiology. We used microarray technology (Affymetrix HG-U133A GeneChips) to determine the expression of approximately 22 000 mRNA transcripts in post-mortem brain tissue (dorsolateral prefrontal cortex and orbitofrontal cortex) from patients with bipolar disorder and matched healthy controls. Experiment Overall Design: Refer to individual Series
2008-06-13 | E-GEOD-5392 | biostudies-arrayexpress